MmuALTD1016835-2/2 @ mm10
Alternative 5'ss
Gene
ENSMUSG00000029661 | Col1a2
Description
collagen, type I, alpha 2 [Source:MGI Symbol;Acc:MGI:88468]
Coordinates
chr6:4537778-4538810:+
Coord C1 exon
chr6:4537778-4537990
Coord A exon
chr6:4537991-4538036
Coord C2 exon
chr6:4538626-4538810
Length
46 bp
Sequences
Splice sites
5' ss Seq
GCGGTGGGT
5' ss Score
6.6
3' ss Seq
GGATTTTCTTTCCTAAACAGATT
3' ss Score
8.7
Exon sequences
Seq C1 exon
GGTCCCCCTGGTCCCCCTGGACCTCCTGGTCCTCCTGGTGTCAGCGGAGGTGGCTATGACTTTGGTTTTGAAGGAGACTTCTACAGGGCTGACCAGCCTCGCTCCCAGCCTTCACTCAGACCCAAGGACTATGAAGTTGATGCAACTCTGAAATCTCTCAATAACCAGATTGAGACCCTTCTCACTCCTGAAGGCTCTAGAAAGAACCCTGCT
Seq A exon
CGCACGTGCCGGGACTTAAGACTCAGCCACCCAGAGTGGAACAGCG
Seq C2 exon
ATTACTACTGGATTGACCCTAACCAAGGATGTACTATGGATGCCATCAAAGTGTACTGTGATTTCTCTACTGGTGAAACCTGCATCCAGGCCCAACCTGTAAACACCCCAGCGAAGAACTCATACAGCCGCGCCCAGGCCAACAAGCATGTCTGGTTAGGAGAGACTATCAATGGTGGCAGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029661-81-75,82-75-2/2
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.897 A=NA C2=0.129
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(34.3=27.6),PF0141013=COLFI=PU(12.4=31.0)
A:
NA
C2:
PF0141013=COLFI=FE(28.1=100)
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGGCTCTAGAAAGAACCCTGCT
R:
CTGGGGTGTTTACAGGTTGGG
Band lengths:
133-179
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types